Ewan Birney

NAME

Bio::Search::Hit::HitI - Interface for a hit in a similarity search result

SYNOPSIS

Bio::Search::Hit::HitI objects should not be instantiated since this module defines a pure interface.

Given an object that implements the Bio::Search::Hit::HitI interface, you can do the following things with it:

    $hit_name = $hit->name();

    $desc = $hit->description();

    $len = $hit->length

    $alg = $hit->algorithm();

    $score = $hit->raw_score();

    $significance = $hit->significance();

    while( $hsp = $obj->next_hsp()) { ... }

    while( $hsp = $obj->next_hsp()) { ... }

DESCRIPTION

    Bio::Search::Hit::* objects are data structures that contain information
about specific hits obtained during a library search.  Some information will
be algorithm-specific, but others will be generally defined.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Aaron Mackey, Steve Chervitz

Email amackey@virginia.edu (original author) Email sac@bioperl.org

COPYRIGHT

Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

name

 Title   : name
 Usage   : $hit_name = $hit->name();
 Function: returns the name of the Hit sequence
 Returns : a scalar string
 Args    : none

description

 Title   : description
 Usage   : $desc = $hit->description();
 Function: Retrieve the description for the hit
 Returns : a scalar string
 Args    : none

accession

 Title   : accession
 Usage   : $acc = $hit->accession();
 Function: Retrieve the accession (if available) for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none

length

 Title   : length
 Usage   : my $len = $hit->length
 Function: Returns the length of the hit 
 Returns : integer
 Args    : none

algorithm

 Title   : algorithm
 Usage   : $alg = $hit->algorithm();
 Function: Gets the algorithm specification that was used to obtain the hit
           For BLAST, the algorithm denotes what type of sequence was aligned 
           against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated 
           dna-prt, TBLASTN prt-translated dna, TBLASTX translated 
           dna-translated dna).
 Returns : a scalar string 
 Args    : none

raw_score

 Title   : raw_score
 Usage   : $score = $hit->raw_score();
 Function: Gets the "raw score" generated by the algorithm.  What
           this score is exactly will vary from algorithm to algorithm,
           returning undef if unavailable.
 Returns : a scalar value
 Args    : none

significance

 Title   : significance
 Usage   : $significance = $hit->significance();
 Function: Used to obtain the E or P value of a hit, i.e. the probability that
           this particular hit was obtained purely by random chance.  If
           information is not available (nor calculatable from other
           information sources), return undef.
 Returns : a scalar value or undef if unavailable
 Args    : none

next_hsp

 Title    : next_hsp
 Usage    : while( $hsp = $obj->next_hsp()) { ... }
 Function : Returns the next available High Scoring Pair
 Example  : 
 Returns  : Bio::Search::HSP::HSPI object or null if finished
 Args     : none

hits

 Title   : hits
 Usage   :
 Function:
 Returns : 
 Args    :